User: Frederico Moraes Ferreira

Reputation:
100
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Trusted
Location:
Brazil
Last seen:
8 months, 4 weeks ago
Joined:
5 years, 5 months ago
Email:
f*********@usp.br

Posts by Frederico Moraes Ferreira

<prev • 23 results • page 1 of 3 • next >
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Comment: C: readCufflinks problem with extdata
... The same issue here: R » dir = "../" R » outdir = "BM_I_vs_SP_I" R » cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE) Creating database ..//BM_I_vs_SP_I/cuffData.db Reading Run Info File ..//BM_I_vs_SP_I/run.info Writing runInfo Table Reading Read Group Info ..//BM_I_vs_SP_I ...
written 8 months ago by Frederico Moraes Ferreira100
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Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Could someone, please, possibly provide more information on patching the qPCRset.R file?  Shouldn't be such patch in Bioconductor repo? Any help is appreciated.   ...
written 13 months ago by Frederico Moraes Ferreira100
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HTqPCR package: problems with the limmaCtData function
... Hi list,  I'm using the HTqPCR package to read data, set categories, normalize and so on. However, I'm having problems with the HTqPCR limma function "limmaCtData". normFilt is a normalized and filtered qPCRset >>show(normFilt) ...
htqpcr written 15 months ago by Frederico Moraes Ferreira100
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Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Just to confirm this issue. The same happens not only on sub setting a qPCRset but also when you try reassigning samples names. I mean, considering raw a qPCRset, such problem appears if I you rename samples: R »sampleNames(raw) <- rownames(phenoData)  Error in (function (od, vd)  :    object a ...
written 15 months ago by Frederico Moraes Ferreira100
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Comment: C: Affymetrix mogene 2.0 annotation data vs 2.1
... This information is true. I just checked it with Affymetrics. MoGene2.1st annotation CANNOT be used for MoGene2.0st plataform.      ...
written 22 months ago by Frederico Moraes Ferreira100
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select samples for qPCR
... Hi there,  It came about a situation which I have more samples that I can afford to proceed with the qPCR experiments. I have three clinically separated groups with more than 20 samples. So, the idea would be to select 7-8 sample from each group. For that, I have three numerical variable such as ag ...
qpcr sample written 3.1 years ago by Frederico Moraes Ferreira100
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Comment: C: HTqPCR- gene names not maintained in limmaCtData
... Hi there,  Exactly the same problem here. It would be really nice if  HTqPCR maintainers fix this. From the vignette looks like the ttestCtData and mannwhitneyCtData functions output feature names, however they don't at least for HTqPCR_1.22.0 ...
written 3.2 years ago by Frederico Moraes Ferreira100
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Answer: A: which Agilent annotation db?
... Dear Axel,  Thanks for replay. It seems there isn't a specific database for the Agilent kit that.  So, I have been using the mouse whole genome database mgug4122a. However, I was able to map about 20% of the probes only. I was wondering if perhaps I can map more probes with a different database.   ...
written 3.4 years ago by Frederico Moraes Ferreira100
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which Agilent annotation db?
... Hi there,  I need to map probes to genes, but not sure which mouse Agilent annotation data base to pick. Possible options are mgug4104a, mgug4120a, mgug4121a, mgug4122a. The experiment was performed with the following SurePrint G3 Mouse GE 8x60K Microarray Kit - G4852A. However, I could not find th ...
annotation agilent written 3.4 years ago by Frederico Moraes Ferreira100
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Answer: A: pytables to R
... Have you thought about using rpy2 module? Have a look at http://rpy.sourceforge.net/ Inside the python environment you can read the desirable chunk of your hdf5 file and flush it as R object to a file with rpy2. The Pandas python modules has some methods to deal with hdf5 files. I've never done thi ...
written 3.7 years ago by Frederico Moraes Ferreira100

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Popular Question 22 months ago, created a question with more than 1,000 views. For which Agilent annotation db?
Popular Question 22 months ago, created a question with more than 1,000 views. For heatmap.2: Colv dendrogram doesn't match size of x

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